Contacts of the helix formed by residues 9 - 26 (chain o) in PDB entry 3J9X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 9 (chain o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K THR* 5.5 12.8 - - - +
51K LYS* 6.0 4.9 - - - -
8o ARG* 1.3 74.9 - - - +
10o TYR* 1.3 60.0 + - - +
11o SER* 3.6 9.8 + - - -
12o GLN* 2.8 35.9 + - - +
13o ARG* 2.8 26.4 + - - +
53p THR* 4.3 3.8 - - - -
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Residues in contact with TYR 10 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K PRO* 4.9 12.1 - - + -
10L TYR* 2.8 43.6 + + - -
11L SER* 5.5 0.3 - - - -
9o SER* 1.3 73.7 - - - +
11o SER* 1.3 70.5 + - - +
13o ARG* 3.0 4.7 + - + -
14o TYR* 2.9 47.0 + + + +
45p PHE* 4.1 0.7 - + - -
46p GLN* 3.3 35.7 + - - +
49p VAL* 3.8 16.6 - - + -
50p PRO* 3.5 40.4 - - + -
53p THR* 3.5 32.5 - - + +
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Residues in contact with SER 11 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K GLN* 5.1 8.5 - - - -
46K GLN* 2.8 48.7 + - - +
47K THR* 4.1 5.0 - - - -
50K PRO* 4.8 0.7 - - - +
10L TYR* 5.0 1.6 + - - -
9o SER* 3.2 9.6 + - - -
10o TYR* 1.3 87.2 - - - +
12o GLN* 1.3 59.9 + - - +
14o TYR* 4.0 3.8 - - - +
15o ALA* 3.0 30.6 + - - +
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Residues in contact with GLN 12 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047 T 4.5 4.0 + - - -
43K GLN* 6.1 2.5 - - - +
40n VAL* 5.2 2.1 - - - +
43n GLN* 5.3 8.6 - - + +
44n ASN* 2.9 34.1 + - - +
47n THR* 4.6 18.5 + - - +
48n ASN* 5.2 1.8 - - - +
7o SER 4.2 4.9 + - - +
8o ARG* 3.6 29.5 - - - +
9o SER* 2.8 39.1 + - - +
11o SER* 1.3 78.0 - - - +
13o ARG* 1.3 66.7 + - - +
15o ALA* 3.7 4.7 - - - +
16o LYS* 3.2 23.9 + - - +
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Residues in contact with ARG 13 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037 A 3.4 54.2 + - + +
1047 T 3.6 40.0 + - - -
2468 T 4.1 7.5 + - - -
2478 A 5.3 5.9 + - - -
8o ARG* 4.1 6.5 - - + +
9o SER 2.8 22.3 + - - +
10o TYR* 3.0 10.1 + - + +
12o GLN* 1.3 72.3 - - - +
14o TYR* 1.3 62.4 + - - +
16o LYS 3.7 0.2 + - - -
17o TRP* 3.1 23.1 + - - +
45p PHE* 4.6 8.0 - - + -
49p VAL* 3.7 20.4 + - + +
52p PHE* 4.6 4.6 - - - +
53p THR* 2.8 45.2 + - - +
56p ASN* 4.3 10.6 - - - +
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Residues in contact with TYR 14 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K GLN* 6.2 1.6 - - - -
10L TYR* 5.5 1.6 - - - -
10o TYR* 2.9 36.1 + + + +
11o SER* 4.1 3.1 - - - +
13o ARG* 1.3 77.0 - - - +
15o ALA* 1.3 69.5 + - - +
17o TRP* 3.1 16.1 + + - +
18o GLN* 2.7 55.7 + - + +
42p GLN* 3.7 9.2 + - - +
45p PHE* 3.4 35.7 - + + -
46p GLN* 2.9 36.4 + - + -
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Residues in contact with ALA 15 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40n VAL* 4.0 21.2 - - + +
11o SER 3.0 21.1 + - - +
12o GLN* 3.4 7.6 + - - +
14o TYR* 1.3 81.6 - - - +
16o LYS* 1.3 62.0 + - - +
18o GLN* 3.3 6.1 + - - +
19o ALA* 3.2 19.9 + - - +
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Residues in contact with LYS 16 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037 A 3.3 40.9 + - - +
1047 T 4.3 13.8 + - - +
2378 A 3.8 37.2 + - - +
2388 T 2.8 36.1 + - - +
37n VAL* 4.9 8.1 - - + -
40n VAL* 3.9 18.1 - - + +
44n ASN* 5.0 3.4 - - - +
8o ARG* 6.0 0.2 - - - +
12o GLN 3.2 13.9 + - - +
15o ALA* 1.3 77.6 - - - +
17o TRP* 1.3 66.6 + - - +
19o ALA* 3.1 4.3 + - - +
20o LYS* 3.0 24.9 + - + +
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Residues in contact with TRP 17 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017 A 5.3 0.4 - - - -
1027 T 3.6 19.8 + - + +
1037 A 3.5 29.5 - - - +
2488 T 2.9 36.6 + - + -
13o ARG 3.1 18.9 + - - +
14o TYR* 3.1 22.8 + + - +
16o LYS* 1.3 74.7 - - - +
18o GLN* 1.3 93.1 + - - +
20o LYS* 3.4 1.7 + - - +
21o PHE* 2.9 52.4 + + + +
41p ALA* 4.1 21.3 - - + -
42p GLN* 4.3 5.8 - - + -
45p PHE* 3.5 45.4 - + + -
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Residues in contact with GLN 18 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14o TYR* 2.7 50.4 + - + +
15o ALA* 3.5 11.2 - - - +
17o TRP* 1.3 88.0 - - - +
19o ALA* 1.3 62.1 + - - +
21o PHE* 3.2 6.7 + - - +
22o ASN* 2.9 63.7 + - - +
42p GLN* 3.2 35.5 - - - +
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Residues in contact with ALA 19 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36n ASN* 3.4 34.4 - - - +
37n VAL* 3.7 17.5 - - + -
40n VAL* 4.3 6.5 - - + -
15o ALA 3.2 9.4 + - - +
16o LYS* 3.1 9.5 + - - +
18o GLN* 1.3 80.5 - - - +
20o LYS* 1.3 58.1 + - - +
22o ASN* 3.5 8.1 + - - +
23o ALA* 3.1 26.9 + - - +
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Residues in contact with LYS 20 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027 T 3.5 40.8 + - + +
1037 A 3.1 30.2 + - - +
2388 T 2.8 31.3 + - - +
2398 A 3.2 27.0 + - - -
33n ILE* 4.0 21.1 - - + -
37n VAL* 3.7 15.5 - - + -
16o LYS* 3.0 17.9 + - + +
17o TRP 3.9 2.9 - - - +
19o ALA* 1.3 73.8 - - - +
21o PHE* 1.3 66.1 + - - +
23o ALA* 3.3 4.3 + - + +
24o PHE* 3.0 24.4 + - - +
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Residues in contact with PHE 21 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017 A 6.1 4.0 - + - -
1027 T 5.6 2.4 - - - +
2488 T 5.8 0.4 - - - -
2498 A 4.5 23.8 - - - -
17o TRP* 2.9 46.8 + + + +
18o GLN* 3.6 10.8 - - - +
20o LYS* 1.3 78.4 - - - +
22o ASN* 1.3 71.8 + - - +
24o PHE* 3.3 11.7 + + - +
25o SER* 3.1 23.4 + - - -
34p LEU* 4.1 31.4 - - + -
37p VAL* 4.6 4.7 - - + -
38p SER* 3.6 37.5 - - - -
41p ALA* 4.3 11.4 - - + -
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Residues in contact with ASN 22 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32n THR* 5.2 0.2 - - - +
36n ASN* 4.0 11.9 - - - +
18o GLN* 2.9 52.4 + - - +
19o ALA* 3.6 8.3 - - - +
21o PHE* 1.3 80.3 - - - +
23o ALA* 1.3 62.9 + - - +
25o SER* 2.6 25.9 + - - -
26o ASN* 3.6 4.0 + - - +
38p SER* 5.5 2.4 + - - -
42p GLN* 4.7 3.6 + - - -
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Residues in contact with ALA 23 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32n THR* 3.6 14.8 - - + +
33n ILE* 3.8 28.0 - - + -
36n ASN* 3.4 16.8 - - - +
19o ALA 3.1 13.0 + - - +
20o LYS* 3.5 10.8 - - - +
22o ASN* 1.3 78.1 - - - +
24o PHE* 1.3 63.6 + - - +
26o ASN* 3.1 21.8 + - - +
29o VAL* 3.5 10.4 - - - +
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Residues in contact with PHE 24 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017 A 3.7 52.9 - - + -
1027 T 4.6 8.3 - - - +
2498 A 6.3 0.2 - - - -
20o LYS 3.0 18.0 + - - +
21o PHE* 3.7 12.1 - + - +
23o ALA* 1.3 76.8 - - - +
25o SER* 1.3 62.7 + - - +
26o ASN 3.0 1.8 + - - -
29o VAL* 4.0 6.1 - - - -
30o ALA* 3.3 44.8 + - + +
33o ILE* 4.3 14.4 - - + -
34o LEU* 4.0 23.3 - - + -
24p PHE* 4.4 8.5 - + - -
34p LEU* 3.4 30.3 - - + -
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Residues in contact with SER 25 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21o PHE* 3.1 15.0 + - - -
22o ASN* 2.6 24.1 + - - -
24o PHE* 1.3 76.4 - - - +
26o ASN* 1.3 61.7 + - - +
27o PRO* 3.2 4.3 - - - +
30o ALA* 5.0 0.4 - - - -
31p SER* 3.5 21.1 - - - +
34p LEU* 3.9 36.6 - - - -
35p SER* 4.6 6.1 - - - -
38p SER* 4.6 8.1 + - - -
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Residues in contact with ASN 26 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28n THR* 4.9 3.2 - - - +
32n THR* 4.0 19.6 + - + +
22o ASN 4.6 1.8 - - - +
23o ALA 3.1 16.0 + - - +
24o PHE 3.0 1.0 + - - -
25o SER* 1.3 78.1 + - - +
27o PRO* 1.4 67.0 - - - +
28o THR* 2.7 31.7 + - - +
29o VAL* 2.7 34.9 + - + -
30o ALA* 2.9 12.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il